Sandbox 1 JBIC



Crystal structure of the zinc, cobalt and iron containing adenylate kinase from Desulfovibrio gigas: a novel metal containing adenylate kinase from Gram-negative bacteria
A. Mukhopadhyay, A.V. Kladova, S.A. Bursakov, O. Yu. Gavel, J.J. Calvete, V.L. Shnyrov, I. Moura, J.J.G. Moura, M.J. Romão, J. Trincão (Abstract)

Molecular Tour Adenylate kinase (ATP:AMP phosphotransferase, EC 2.7.4.3; AK) is an essential catalyst for cellular growth and multiplication. AK belongs to a family of enzymes essential to life, and is highly abundant inside the cell. It is involved in the reversible transfer of the terminal phosphate group from Mg2+ATP to Mg2+AMP with high energy turnover: Mg2+ATP + AMP&#8596;Mg2+ADP + ADP.

Adenylate kinases (AK) from Gram-negative bacteria are generally devoid of metal ions in their LID domain. However, three metal ions, zinc, cobalt and iron, have been found in AK from Gram-negative bacteria. Crystal structures of substrate-free AK from Desulfovibrio gigas with three different metal ions: Zn2+, Zn-AK (2xb4); Co2+, Co-AK (3l0s) and Fe2+, Fe-AK (3l0p) bound in its LID domain have been determined by X-ray crystallography. All three crystal structures are very similar to each other with the same LID domain topology, the only change being the presence of the different metal atoms.

The structures of Zn-, Co- and Fe-AK contain the characteristic LID domain (residues 125-163) and Core (residues 1-124 and 164-223) domains , which also include the AMP binding region. The LID domain harbors the Cys129-X5-His135-X15-Cys151-X2-Cys154- motif, which is responsible for metal binding in a tetrahedral fashion. In the absence of any substrate, the LID domain of all holo forms of AK was present in a fully open conformational state. The Core domain is connected to the LID by residues 116-123 and 165-173. This Core domain mainly consists of a five stranded beta sheet surrounded by 5 helices that keep the integrity of the tertiary structure of the enzyme. A Walker motif with conserved sequence; G - X - X - G - X - G - K is present in the N-terminal region The structures presented herein further reinforce the notion that the metal ion is purely structural, contributing to the stability of the LID domain.